As the impending effects of global warning become clearer, there has been an increasing interest in finding ways to reduce our emissions of greenhouse gasses, such a carbon dioxide. While nature has already optimized several routes for converting carbon dioxide into useful compounds, selective pressures in nature are not the same as design parameters for industrial applications.
The idea that proteins are nature's catalysts (enzymes) was born in the early 1800s, and solidified by Payen and Persoz, who are credited as being the first to isolate and characterize an enzyme (amylase, then called diastase). This work demonstrated that an isolated protein could convert starch into sugar (Payen, A., and J. F. Persoz, “Mémoire Sur La Diastase, Les Principaux Produits De Ses Réactions, Et Leurs Applications Aux Arts Industriels,” Annales de Chimie et de Physique 2:73-92, 1833; Segel, I. H., “Enzyme Kinetics: Behavior and Analysis of Rapid Equilibrium and Steady State Enzyme Systems,” New York: Wiley; 1975). Since then over 280 thousand enzymes have been identified, which represent almost 5 thousand different chemical transformations (Chang, A., et al. “BRENDA, AMENDA and FRENDA the Enzyme Information System: New Content and Tools in 2009,” Nucl. Acids Res. 2008). In addition to the vast chemical space covered by enzymes, they are also some of the world's most efficient catalysts, capable of being either highly regio-stereo-specific (Karsten, W. E., et al., “Kinetic-Studies of L-Aspartase from Escherichia-Coli—Substrate Activation,” Biochem. 25:1299-1303, 1986; Michel, C., et al., “Adenosylcobalamin and Cob(II)Alamin as Prosthetic Groups of 2-Methyleneglutarate Mutase from Clostridium-Barkeri,” Eur. J. Biochem. 205:767-773, 1992) or being relatively non-specific (Coleman, J. E., and P. Gettins, “Alkaline-Phosphatase, Solution Structure, and Mechanism,” Advances in Enzymology and Related Areas of Molecular Biology 55:381-452, 1983; Sun, H. W., et al., “Enlarging the Substrate Binding Pocket of Yeast Alcohol Dehydrogenase-we,” FASEB Journal 5:A1150-A1150, 1991; Green, D. W., et al., “Inversion of the Substrate-Specificity of Yeast Alcohol-Dehydrogenase,” J. Biol. Chem. 268:7792-7798, 1993; Mast, N., et al. “Broad Substrate Specificity of Human Cytochrome P450 46a1 Which Initiates Cholesterol Degradation in the Brain,” Biochem. 42:14284-14292, 2003) while catalyzing difficult chemical transformations with rate enhancements of 1019 in mild and ecologically friendly conditions (Wolfenden, R., and M. J. Snider, “The Depth of Chemical Time and the Power of Enzymes as Catalysts,” Accounts of Chemical Research 34:938-945, 2001).
Due to this impressive ability to catalyze reactions under mild conditions, enzymes have consistently gained popularity in the fields of industry, medicine, and the basic sciences as tools for performing chemical transformations. One profound example is glucose isomerase, which is currently used in the food industry to produce over a million tons of fructose per year (Powell, K. A., et al., “Directed Evolution and Biocatalysis,” Angewandte Chemie—International Edition 40:3948-3959, 2001). Yet even with the vast number of enzymes provided by nature, there are numerous important applications for which there is no biological catalyst capable of performing the desired chemical transformation. In order to address these needs, scientists have begun engineering enzymes in order to alter their properties to match the desired need (Ashworth, J., et al. “Computational Redesign of Endonuclease DNA Binding and Cleavage Specificity,” Nature 441:656-659, 2006; Shah, K., et al., “Engineering Unnatural Nucleotide Specificity for Rous Sarcoma Virus Tyrosine Kinase to Uniquely Label Its Direct Substrates,” Proc. Nat'l Acad. Sci. USA 94:3565-3570, 1997; Chang, T. K., et al. “Subtiligase: a Tool for Semisynthesis of Proteins,” Proc. Nat'l Acad. Sci. USA 91:12544-12548, 1994; Jackson, D. Y., et al. “A Designed Peptide Ligase for Total Synthesis of Ribonuclease A With Unnatural Catalytic Residues,” Science 266:243-247, 1994; Black, M. E., et al. “Creation of Drug-Specific Herpes Simplex Virus Type 1 Thymidine Kinase Mutants for Gene Therapy,” Proc. Nat'l Acad. Sci. USA 93:3525-3529, 1996; Crameri, A., et al. “Molecular Evolution of an Arsenate Detoxification Pathway by DNA Shuffling,” Nat. Biotechnol. 15:436-438, 1997; Braha, O., et al. “Designed Protein Pores as Components for Biosensors,” Chem. Biol. 4:497-505, 1997). While there are examples of success stories, often success is limited by an incomplete understanding of the enzyme's mechanism and the inability to sample the practically limitless number of amino acid sequence combinations from which only a few code for the optimal protein to catalyze the reaction of interest.
Despite the advances in the art regarding modified and optimized enzymes, a need remains for novel enzyme catalysts and methods for their use to convert abundant C1 carbon sources, such as carbon dioxide, into useful hydrocarbons, such as for energy sources. The invention set forth in this disclosure addresses this need and provides further related advantages.